[gmx-users] All bulk is moving during Umbrella sampling

[Justin Lemkul]

On 6/8/15 10:00 AM, gozde ergin wrote:
> Justin, thank you for the advice.
>
> But if I apply a force to keep molecules within a layer, how I will extract
> this force effect on PMF?
>

There's likely some simple formula for correcting for this effect; surely 
someone has published such cases.

-Justin

> On Sun, Jun 7, 2015 at 3:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/6/15 2:57 PM, gozde ergin wrote:
>>
>>> Actually I know I need to do something like this however I don't know how
>>> to do it.
>>> Could anybody give a hint how this approach can be realized in GROMACS?
>>> I could not find a clear answer in manual.
>>>
>>>
>> The key is the definition of the restraint reference coordinates.  To keep
>> molecules within a layer from zero to some value z, you need to create a
>> reference coordinate file in which the z-coordinate of the restrained atoms
>> are all equal to z/2, such that the restraint will take effect at +z and
>> zero.  This coordinate file is only to be used for grompp -r as it is
>> obviously nonphysical, but it defines the reference positions for the
>> restraints.
>>
>> Then set the correct "layer" geometry (g=5 for a layer along z) and
>> specify the value of z at which the restraint is applied.  This also needs
>> to be done with no pressure coupling along z, which is probably the case
>> already for what you're doing.
>>
>> -Justin
>>
>>
>>   On Thu, Jun 4, 2015 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 6/4/15 10:43 AM, gozde ergin wrote:
>>>>
>>>>   Hi all,
>>>>>
>>>>> I am doing some umbrella sampling simulation in order to estimate the
>>>>> PMF
>>>>> profile of the system.
>>>>> While doing this simulations I did:
>>>>>
>>>>> -- Simulated the system in x*y*z box.
>>>>> -- In order to have a gas phase I expanded the z coordinate to 5z and
>>>>> simulate the system in x*y*5z
>>>>> -- Minimization
>>>>> -- Equilibration
>>>>> -- Pulling
>>>>> -- Than umbrella sampling.
>>>>>
>>>>> During the umbrella sampling all of bulk molecules moved on z direction.
>>>>> However the distances between the COM of pulled molecule and COM of mass
>>>>> stays constant. It is not a big problem for estimating the PMF but it
>>>>> is a
>>>>> problem when I want to calculate the pressure and density profile of the
>>>>> system.
>>>>>
>>>>> Do you have any suggestion to prevent the bulk molecules moving inside
>>>>> the
>>>>> box?
>>>>>
>>>>>
>>>>>   Use a flat-bottom restraint to confine the bulk to one region of the
>>>> box.
>>>> Otherwise, they will naturally have a tendency to fill up the available
>>>> space.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================